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Fluorine in PDB 3elc: Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Clycodiphosphate Synthase Complexed with Ligand

Enzymatic activity of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Clycodiphosphate Synthase Complexed with Ligand

All present enzymatic activity of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Clycodiphosphate Synthase Complexed with Ligand:
4.6.1.12;

Protein crystallography data

The structure of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Clycodiphosphate Synthase Complexed with Ligand, PDB code: 3elc was solved by W.N.Hunter, N.L.Ramsden, V.Ulaganathan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 104.676, 54.833, 88.506, 90.00, 99.66, 90.00
R / Rfree (%) 20.8 / 29.1

Other elements in 3elc:

The structure of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Clycodiphosphate Synthase Complexed with Ligand also contains other interesting chemical elements:

Zinc (Zn) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Clycodiphosphate Synthase Complexed with Ligand (pdb code 3elc). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Clycodiphosphate Synthase Complexed with Ligand, PDB code: 3elc:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 3elc

Go back to Fluorine Binding Sites List in 3elc
Fluorine binding site 1 out of 3 in the Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Clycodiphosphate Synthase Complexed with Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Clycodiphosphate Synthase Complexed with Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:47.5
occ:1.00
 F1 A:F01901 0.0 47.5 1.0
C8 A:F01901 1.3 45.9 1.0
C7 A:F01901 2.3 45.5 1.0
C9 A:F01901 2.4 46.3 1.0
N2 A:F01901 2.7 46.3 1.0
C A:THR132 2.9 37.9 1.0
O A:ALA100 3.0 34.1 1.0
N A:THR133 3.1 38.1 1.0
O A:THR132 3.2 38.5 1.0
CG2 A:THR133 3.2 39.1 1.0
CA A:THR132 3.3 37.6 1.0
N A:THR132 3.5 36.6 1.0
N1 A:F01901 3.6 46.2 1.0
N3 A:F01901 3.7 48.1 1.0
CA A:THR133 3.8 38.9 1.0
CB A:THR133 4.0 38.6 1.0
C A:ALA131 4.1 36.9 1.0
C6 A:F01901 4.1 48.1 1.0
O A:HOH928 4.2 34.4 1.0
C A:ALA100 4.3 34.7 1.0
O A:ALA131 4.5 37.3 1.0
CB A:ALA131 4.5 36.8 1.0
O5 A:F01901 4.6 54.2 1.0
OG1 A:THR133 4.7 39.1 1.0
N A:ALA100 4.7 33.9 1.0
CB A:THR132 4.8 37.6 1.0
C1 A:F01901 4.9 47.7 1.0
O4 A:F01901 4.9 46.4 1.0
CA A:ALA131 4.9 37.0 1.0

Fluorine binding site 2 out of 3 in 3elc

Go back to Fluorine Binding Sites List in 3elc
Fluorine binding site 2 out of 3 in the Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Clycodiphosphate Synthase Complexed with Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Clycodiphosphate Synthase Complexed with Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F902

b:68.3
occ:1.00
 F1 B:F01902 0.0 68.3 1.0
C8 B:F01902 1.3 67.8 1.0
C9 B:F01902 2.3 67.9 1.0
C7 B:F01902 2.4 67.9 1.0
N2 B:F01902 2.8 67.3 1.0
CG2 B:THR133 2.9 45.2 1.0
C B:THR132 3.1 44.3 1.0
N B:THR133 3.2 44.9 1.0
O B:THR132 3.4 44.7 1.0
O B:ALA100 3.4 47.9 1.0
CA B:THR132 3.4 43.5 1.0
N3 B:F01902 3.6 68.3 1.0
N1 B:F01902 3.6 68.3 1.0
N B:THR132 3.7 42.4 1.0
CA B:THR133 3.9 45.8 1.0
CB B:THR133 3.9 45.6 1.0
C B:ALA131 4.1 42.2 1.0
C6 B:F01902 4.1 68.5 1.0
CE B:LYS104 4.3 58.3 1.0
O B:ALA131 4.3 42.5 1.0
OG1 B:THR133 4.4 46.0 1.0
NZ B:LYS104 4.4 57.2 1.0
O5 B:F01902 4.4 69.5 1.0
CB B:ALA131 4.5 41.6 1.0
C B:ALA100 4.7 47.9 1.0
C1 B:F01902 4.8 68.5 1.0
O B:GLN101 4.9 49.8 1.0
CA B:ALA131 4.9 41.7 1.0
CB B:THR132 4.9 43.4 1.0
O4 B:F01902 4.9 67.9 1.0

Fluorine binding site 3 out of 3 in 3elc

Go back to Fluorine Binding Sites List in 3elc
Fluorine binding site 3 out of 3 in the Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Clycodiphosphate Synthase Complexed with Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Clycodiphosphate Synthase Complexed with Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F903

b:67.5
occ:1.00
 F1 C:F01903 0.0 67.5 1.0
C8 C:F01903 1.3 66.9 1.0
C9 C:F01903 2.4 66.8 1.0
C7 C:F01903 2.4 66.3 1.0
N2 C:F01903 2.7 65.1 1.0
C C:THR132 2.8 45.5 1.0
O C:THR132 2.9 45.6 1.0
CG2 C:THR133 2.9 46.4 1.0
O C:ALA100 3.1 43.9 1.0
N C:THR133 3.2 45.7 1.0
CA C:THR132 3.3 45.3 1.0
N C:THR132 3.4 44.5 1.0
N3 C:F01903 3.7 66.3 1.0
N1 C:F01903 3.7 66.3 1.0
CA C:THR133 3.8 46.2 1.0
CB C:THR133 3.9 46.0 1.0
C C:ALA131 4.0 44.0 1.0
O C:HOH930 4.0 59.6 1.0
C6 C:F01903 4.2 66.2 1.0
C C:ALA100 4.3 43.7 1.0
O C:ALA131 4.4 44.3 1.0
CB C:ALA131 4.5 43.1 1.0
OG1 C:THR133 4.7 46.5 1.0
N C:ALA100 4.8 42.0 1.0
CB C:THR132 4.8 45.4 1.0
CA C:ALA131 4.8 43.4 1.0
C1 C:F01903 4.9 66.1 1.0
O4 C:F01903 4.9 64.9 1.0
O5 C:F01903 5.0 67.5 1.0
O C:GLN101 5.0 46.1 1.0

Reference:

N.L.Ramsden, L.Buetow, A.Dawson, L.A.Kemp, V.Ulaganathan, R.Brenk, G.Klebe, W.N.Hunter. A Structure-Based Approach to Ligand Discovery For 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase: A Target For Antimicrobial Therapy J.Med.Chem. V. 52 2531 2009.
ISSN: ISSN 0022-2623
PubMed: 19320487
DOI: 10.1021/JM801475N
Page generated: Mon Jul 14 16:06:55 2025

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